Expression vector

ABSTRACT

An expression vector including two separately inducible converging promoters P1 and P2, and expression system including such an expression vector and an additional regulator vector, a method of protein expression using such an expression system, and a method of investigating (meta)genome libraries using such an expression system.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. patent application Ser. No.13/162,204, filed Jun. 16, 2011, which is a continuation ofInternational patent application no. PCT/EP2009/008977, filed Dec. 15,2009, which claims priority from European patent application no.08021794.6, filed Dec. 16, 2008, the entire disclosure of which isincorporated herein by reference.

BACKGROUND OF THE INVENTION

The invention relates to an expression vector that is suitable forefficient screening of (meta)genome libraries, preferably in Escherichiacoli.

Only about 1-5% of all known microorganisms are at present cultivable inthe laboratory with current methods. Methods have been developed inrecent times which should make it possible to use the genetic resourcesof non-cultivable microorganisms. This field is also called“metagenomics”, with the term “metagenome” denoting the geneticinformation of all organisms of a particular habitat, regardless ofwhether these are cultivable or not.

By direct cloning of the DNA obtained from environmental samples intosuitable vector systems (plasmids, cosmids, BACs, YACs) this resourcebecomes available for easy manipulation in the laboratory. These genebanks (metagenome libraries) can be used for example for searching fornovel enzymes. Finding completely novel enzyme activities requiresactivity-based screening of prepared metagenome libraries. Aprecondition for this is a suitable detection system (agar plate assays,microtitre plate systems), which permits simultaneous screening of thelargest possible number of clones (high-throughput screening).Furthermore, expression of the genes must be provided in a heterologoushost. In addition to E. coli, other organisms such as Streptomyceslividans or Pseudomonas putida are also employed as host in metagenomestudies.

Problems with the metagenome technique relate in particular toexpression of the genes found. These include inadequate transcription,for example because promoters are not recognized, toxicity of theproducts to the host, missing cofactors or chaperones and thereforeincorrect folding of the proteins in the heterologous host, and missingsecretion systems (W. R. Streit et al., Curr Opin Microbiol. 2004, 7(5),492-8).

Conventional (meta)genome libraries for screening in E. coli aregenerally constructed in artificial chromosomes (BAC), cosmid or fosmidsystems or plasmids. Until now, (meta)genomic plasmid libraries havemainly been constructed using conventional cloning vectors, whichgenerally have an individual, comparatively weak promoter (e.g. lacpromoter) or are designed entirely for the use of internal promoters ofthe cloned DNA. This weak promoter was not originally intended forexpression of the cloned DNA, but is present as promoter before the lacZgene, which is often used as marker. In this connection, reference maybe made for example to R. Ranjan et al., Biochem Biophys Res Commun.,2005, 335(1), 57-65; and A. Knietsch et al., Appl Environ Microbiol.,2003, 69(3), 1408-1416.

The relative weakness of the promoter does not have any negativeconsequences in sequence-based screening of the (meta)genome library.However, if the same plasmid libraries are used for screening theactivity of the target proteins encoded by the library, expression ofthe target proteins is then often based on the weak promoter located atthe plasmid. With the cosmid/fosmid systems that are often used, thefunctional expression of the target genes is based exclusively onrecognition and reading of the non-E. coli promoters located on theinserted DNA. In this connection, reference may be made for example toK. S. Hong et al., J Microbiol Biotechnol., 2007, 17(10), 1655-60.

Owing to the weakness of the promoter or the non-recognition of non-E.coli promoters, some of the target proteins are barely expressed, or notat all, so that activity screening of the target proteins is far moredifficult. These limitations make iterative activity screening ofsub-libraries (cluster screening, cf. US 2008/220581=WO 2005/040376)impossible in most cases. Instead, complicated and time-consumingactivity screening with individual clones, e.g. on agar plates, isnecessary.

Another problem in activity screening is that when constructing(meta)genome libraries it is not possible to influence the orientationof the open reading frame (ORF) on the cloned DNA. It is also possiblefor two successive open reading frames to have different directions ofreading. In activity screening with conventional expression vectors, alarge part of the sequence information contained in the (meta)genomelibrary is therefore often lost because the promoter used only coversone of the two possible directions of reading.

U.S. Pat. No. 6,780,405 (=WO 01/83785) discloses a regulated system fordelivery of antigens. In this system, however, the DNA to be cloned intothe insertion sequence is not under the control of both promoters.Instead, one of the two promoters controls the on or a gene forregulating the ori. Such a system is hardly suitable for screeningmetagenome libraries, as only 50% of the sequence information containedis captured.

U.S. Pat. No. 6,030,807 discloses an operon that codes for enzymes thatare linked with the use of L-arabinose. The operon does not, however,have an insertion sequence located between two promoters convergingtowards each other. The system also does not include a vector with twodifferent promoters converging towards each other, between which aninsertion sequence is arranged, in each case downstream.

U.S. Pat. No. 6,977,165 (=WO 02/083910) discloses a method of productionof a vector that includes at least one spliceable intron. The vectorsize is not, however, maximum 3000 bp.

Schmeisser et al., Appl. Microbiol. Biotechnol 2007, 75(5), 955-62 is areview of the subject: Metagenomics, biotechnology with non-cultivablemicrobes. The publication does not contain any information on expressionin plasmids with two promoters converging towards one another, andinducible separately from one another, between which an insertionsequence is arranged, in each case downstream, so that the expression ofa DNA sequence cloned into the insertion sequence is placed under thecontrol of both promoters.

U.S. Pat. No. 7,005,423 (=WO 00/01846) discloses a method foridentifying DNA that is responsible for a particular phenotype. However,that method does not use a vector with promoters that are inducibleseparately from one another, and flow towards one another. It is even aprecondition of the method that both promoters are identical. The vectordoes not comprise at most 3000 bp.

S. Kim et al., Prot. Expr Purif. 2006, 50(1), 49-57 discloses rare codonclusters on the 5′-terminus, which have an influence on heterologousexpression of archaic genes in E. coli. The publication does not,however, contain any mention of an expression vector that comprises twopromoters inducible separately from one another, and converging towardseach other, between which an insertion sequence is arranged, in eachcase downstream, so that the expression of a DNA sequence cloned intothe insertion sequence is placed under the control of both promoters.

F. W. Studier, J. Mol. Biol. 1991, 219(1), 37-44 discloses the use of T7lysozyme bacteriophage for improving an inducible T7 expression system.The system does not, however, have an expression vector that comprisestwo promoters inducible separately from one another, and convergingtowards each other, between which an insertion sequence is arranged, ineach case downstream, so that the expression of a DNA sequence clonedinto the insertion sequence is placed under the control of bothpromoters.

SUMMARY OF THE INVENTION

An object of the invention is to provide an expression system that issuitable for screening, in particular for activity screening, of(meta)genome libraries and has advantages over the systems of the priorart.

Another object is to provide an expression system that is characterizedby a high cloning efficiency linked to efficient, controllableexpression.

A further object of the invention is to provide an expression systemwhich captures as large a proportion as possible of the sequenceinformation contained in the (meta)genome library.

These and other objects have been achieved by the invention as describedand claimed hereinafter.

A first aspect of the invention relates to an expression vectorcomprising two promoters P₁ and P₂, inducible separately from oneanother, and converging towards each other, wherein preferably aninsertion sequence is arranged between P₁ and P₂, in each casedownstream, so that the expression of a DNA sequence cloned into theinsertion sequence is placed under the control of P₁ and P₂; wherein theinsertion sequence is a polylinker and/or a sequence that makesintegration of DNA sequences by recombination possible; and wherein theexpression vector without insertion sequence comprises altogether atmost 3000 bp.

In this connection, “under the control of P₁ and P₂” means that theexpression of the cloned, double-stranded DNA sequence can be controlledby P₁ and P₂. One strand of the cloned, double-stranded DNA sequence iscontrolled by P₁ and the strand of the cloned, double-stranded DNAsequence complementary thereto is controlled by P₂. Control is effectedpreferably in the sense of an operon.

It was found, surprisingly, that the expression vector according to theinvention is particularly suitable for activity screening of(meta)genome libraries, as both directions of reading are covered. Theloss of half of the sequence information contained in the (meta)genomelibrary or the need to screen double the number of clones, as must beaccepted when using conventional expression vectors, can be avoided bythe expression vector according to the invention.

Preferably it is an expression vector for E. coli, with two strongpromoters flanking the multiple cloning site. The promoters areconvergent, i.e. their reading directions converge into each other(face-to-face). The promoters inducible independently of one another arepreferably a T7 promoter and an ara promoter.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows pF2F4, a preferred embodiment of an expression vectoraccording to the invention with <SEQ. ID. NO: 1>. It is an expressionvector for E. coli, in which two strong promoters flank the multiplecloning site. The promoters are convergent, i.e. their readingdirections converge towards each other (face-to-face). The promotersthat are inducible independently of one another are a T7 promoter and anarabinose promoter.

FIG. 2 shows the regulatory plasmid pLac+ with <SEQ. ID. NO: 2>, withwhich, according to the invention, the host organism is preferablytransformed together with the expression vector.

FIG. 3 shows, in connection with example 1, pF2F4 with variouslyoriented alcohol dehydrogenase as reporter gene in E. coli BL21 (DE3)cells, in which pLacI or pLacI+ is propagated simultaneously. Allmeasurements of T7 induction with 1% glucose in the medium, of Arainduction without further glucose addition.

FIG. 4A shows ADH activity, in connection with example 1, pF2F4 withvariously oriented alcohol dehydrogenase as reporter gene in E. coliBL21.

FIG. 4B shows ADH activity, in connection with pF2F4 with variouslyoriented alcohol dehydrogenase as reporter gene in E. coli DH10B. ThepLacI+ plasmid was coexpressed in all assays.

FIG. 5 shows, in connection with example 2, the hit distribution after 3h incubation time in the IPTG-induced cell extract of the rumen libraryin pF2F4. A1 is uninoculated as control.

FIG. 6 is an illustration of a preferred embodiment of the method setforth herein.

In a preferred embodiment of such a method, shown schematically in FIG.6, a library, preferably a (meta)genome library, is prepared (FIG. 6,Step a.)(i)). The library contains the individual variants “A”, “B”, “C”and “D”. According to the invention, this library is transferred into ahost (FIG. 6, Step a.) (ii)).

In Step b.) the clones of one partial library are divided into a firstcompartment (variants “A” and “B” in FIG. 6) and the clones of anotherpartial library into a second compartment (variants “C” and “D” in FIG.6).

DETAILED DESCRIPTION

An expression vector in the sense of the present invention is preferablya DNA sequence, which comprises at least one DNA sequence forreplication in hosts (origin of replication); at least one DNA sequencecoding for a sequence that is suitable for distinguishing hosts thatcontain the expression vector from hosts that do not contain theexpression vector (called “selection marker sequence” within the scopeof the present invention); at least one DNA sequence for insertion offoreign DNA (called “insertion sequence” within the scope of the presentinvention), and at least one DNA sequence that is recognized by an RNApolymerase as transcription start point.

The expression vector according to the invention is suitable for theexpression of peptides or proteins in prokaryotic or eukaryotic systems(hosts).

Preferred prokaryotic systems comprise e.g. bacteria. Preferred bacteriacomprise E. coli, Bacillus sp., Salmonella typhimurium, Staphylococcussp., Pseudomonas sp., Streptomyces sp. and Caulobacter sp. and Borreliasp. Preferred eukaryotic systems comprise e.g. yeasts or SF9 cells,Chinese hamster ovary cells, and other cells of higher organisms.Preferred yeasts comprise Saccharomyces cerevisiae, Schizosaccharomycespombe and Pichia pastoris.

Various aspects can play a role in selection of the host. An importantaspect is the possibility of posttranslational modification of theexpressed peptide/protein in the host cell. Another aspect is thesuitability of the host cell for secretion of the expressedpeptides/proteins. Depending on the biological source of the(meta)genome library, a person skilled in the art can decide which hostappears to be the most suitable for expression. The biological source ofthe (meta)genome library is preferably of purely prokaryotic origin,purely eukaryotic origin or mixed prokaryotic and eukaryotic origin. Thesource can originate for example from a maritime or terrestrialenvironment. Possible examples of suitable sources are organisms thatlive in natural or in artificial, in particular human-influenced,environments. In this connection, comparatively extreme environments mayalso be considered, e.g. volcanoes, hot springs, deserts, iceboundlandscapes, glaciers, areas with unusually high or low pH, areas withhigh radiation exposure or other environmentally exposed biotopes. In apreferred embodiment the sources originate from water treatment works,biofilters or other industrial plant.

Preferably the expression vector according to the invention is aplasmid, e.g. a bacterial plasmid or a yeast plasmid.

In a preferred embodiment the expression vector according to theinvention is a low-copy plasmid (on average <100 plasmids per cell). Inanother preferred embodiment the expression vector according to theinvention is a high-copy plasmid (on average ≥100 plasmids per cell).

The origin of replication (ori) used is relevant for the number ofcopies of the expression vector (not integrated into the chromosome) percell. A large number of on are known to a person skilled in the art andhe is able to select a suitable ori for a particular preferredembodiment. For example, the following ori or ori based on the followingori can be used: E. coli oriC, ColE1-ori or the on from various plasmidsknown by a person skilled in the art such as pUC, pBR322, pGEM, pTZ,pBluescript, pMB1, pSC101, p15a, pR6K, M13-ori, or, for expression inyeast cells, the 2 μm ori or, for expression in other eukaryotic hosts,ori such as SV40-ori.

According to the invention, the expression vector, in particular theexpression plasmid, can also contain several ori, for example 2 ori's.It can, for example, be a combination of a low-copy ori and atemperature-dependent ori or for example ori's that allow propagation invarious host organisms (ori for E. coli and ori for Bacillus sp.).

In addition to plasmids, other vectors may also be considered asexpression vector according to the invention, for example phage,cosmids, phasmids, fosmids, bacterial artificial chromosomes, yeastartificial chromosomes, viruses and retroviruses (for example vaccinia,adenovirus, adeno-associated virus, lentivirus, herpes-simplex virus,Epstein-Barr virus, fowlpox virus, pseudorabies, baculovirus) andvectors derived therefrom.

The expression vector or parts thereof can also be integrated into thegenome.

Any other vector can also be used for production of the expressionvector according to the invention, provided it is replicable and capableof surviving in the selected system (host).

Depending on the (meta)genome library and the host that appears suitablefor expression, selection of the promoters P₁ and P₂ preferably takesplace on a suitable vector.

According to the invention, the term “promoter” comprises anytranscription control sequence that makes it possible to express apeptide or protein in a suitable system, i.e. to transcribe the encodedDNA sequence into RNA and then translate it into the correspondingpeptide or protein sequence. Therefore the term comprises not only thepromoter sequence as such (the binding site of the RNA polymerase), butoptionally, in addition also the enhancer sequence, the operatorsequence, and the like.

All nucleotide sequences in the DNA of the expression vector basicallycome into consideration according to the invention as promoters P₁ andP₂, to which RNA polymerases bind, to start transcription. It ispreferably RNA polymerase of native, naturally occurring organisms, e.g.E. coli. The term also comprises, with respect to a given host,promoters on which RNA polymerases of other organisms bind. For example,the RNA polymerase of the T7-bacteriophage can be co-expressed in E.coli, so as to be able to use the T7 promoter in E. coli, e.g. in E.coli BL21(DE3).

Within the scope of the present invention, “P_(i)” designates optionallyP₁ or P₂.

In a preferred embodiment, P₁ and P₂ are prokaryotic promoters. Inanother preferred embodiment, P₁ and P₂ are eukaryotic promoters.

In a preferred embodiment, P₁ and P₂ can in each case both be addressedby the same organism, i.e. they can perform their functionality in thesame organism and are compatible with the same organism. If, forexample, the expression vector according to the invention is in aparticular microorganism, preferably both promoters P₁ and P₂ can berecognized by the RNA polymerases contained in this microorganism;preferably no further organisms are required for this.

Prokaryotic promoters usually comprise a so-called “−35 element” and theso-called “TATA box” or “Pribnow box”. The consensus sequence for the−35 element comprises the following six nucleotides: TTGACA. Theconsensus sequence for the Pribnow box comprises the six nucleotidesTATAAT. In a preferred embodiment the two promoters P₁ and P₂ differ inat least 1 nucleotide within the whole of these two sequence segments,preferably in at least 2 nucleotides, more preferably at least 3nucleotides, most preferably at least 4 nucleotides and in particular atleast 5 nucleotides. In another preferred embodiment the two promotersP₁ and P₂ differ in at most 5 nucleotides within the whole of these twosequence segments, preferably at most 4 nucleotides, more preferably atmost 3 nucleotides, and most preferably at most 2 nucleotides and inparticular at most 1 nucleotide.

In a preferred embodiment promoter P₁ differs in at least 1 nucleotide,preferably in at least 2 nucleotides, more preferably at least 3nucleotides, and most preferably at least 4 nucleotides and inparticular at least 5 nucleotides from the totality of the twoaforementioned consensus sequences. In another preferred embodimentpromoter P₁ differs in at most 5 nucleotides, preferably at most 4nucleotides, more preferably at most 3 nucleotides, and most preferablyat most 2 nucleotides and in particular at most 1 nucleotide from thetotality of the two aforementioned consensus sequences.

In a preferred embodiment, moreover, promoter P₂ differs in at least 1nucleotide, preferably in at least 2 nucleotides, more preferably atleast 3 nucleotides, and most preferably at least 4 nucleotides and inparticular at least 5 nucleotides from the totality of the twoaforementioned consensus sequences. In another preferred embodiment,moreover, promoter P₂ differs in at most 5 nucleotides, preferably atmost 4 nucleotides, more preferably at most 3 nucleotides, and mostpreferably at most 2 nucleotides and in particular at most 1 nucleotidefrom the totality of the two aforementioned consensus sequences.

The distance between the TATA box and the “−35 box” also has aninfluence on the strength of the promoter. Preferably the distancebetween the TATA box and the “−35 box” of promoter P₁ is 5 to 50 bp,preferably 10 to 30 bp, more preferably 12 to 25 bp, more preferably 15to 20 bp, and most preferably 17 bp. Preferably the distance between theTATA box and the “−35 box” of promoter P₂ is 5 to 50 bp, preferably 10to 30 bp, more preferably 12 to 25 bp, more preferably 15 to 20 bp, andmost preferably 17 bp.

Preferably P₁ and P₂ are externally regulated, i.e. they are functionalpromoters, whose activity can be altered (increased or decreased) by atleast one other element (molecule, component, cofactor, transcriptionfactor, etc.).

Suitable promoters and their partial sequences are known by a personskilled in the art. Examples of suitable promoters comprise viral,vegetable, bacterial, fungal, human and animal promoters, e.g. cos-,tac-, trp-, tet-, trp-tet-, lpp-, lac-, lpp-lac-, laclq-, T7-, T5-, T3-,gal-, trc-, ara-, SP6-, I-PR- or in the I-PL-promoters or partialsequences thereof, which preferably find application in Gram-negativebacteria. Further advantageous promoters are contained for example inthe Gram-positive promoters such as amy, npr, apr and SP02, in the yeastpromoters such as ADC1, MFa, AC, P-60, CYC1, GAPDH or in mammalianpromoters such as CaM-kinase II, CMV, Nestin, L7, BDNF, NF, SV40, RSV,HSV-TK, metallothionein gene, MBP, NSE, beta-globin, GFAP, GAP43,tyrosine hydroxylase, kainate receptor subunit 1, glutamate receptorsubunit B. In principle all natural promoters such as those mentionedabove can be used. Furthermore, synthetic promoters can also be usedadvantageously.

Preferably, P₁≠P₂.

In one preferred embodiment, one of the two promoters P₁ and P₂ isintrinsic with respect to the host used, i.e. at least one intrinsic RNApolymerase of the host is able to bind to the promoter and catalyse atranscription, and the other promoter is extrinsic with respect to thehost used, i.e. no intrinsic RNA polymerase of the host is able to bindto the promoter and catalyse a transcription. In this connection,extrinsic means that the wild type of the host does not code for thisRNA polymerase. In this connection, “catalyse transcription” means thatthe intrinsic RNA polymerases of the host achieve, in a correspondingin-vitro transcription assay, at most 10%, preferably at most 1%, morepreferably at most 0.1% of the transcription rate as the extrinsic RNApolymerase present for this promoter. In this embodiment, thecorrespondingly required extrinsic RNA polymerase is coexpressed.

In another preferred embodiment, gene expression by P₁ is regulated byan individual specific factor, namely by the regulator R₁. In anotherpreferred embodiment, gene expression by P₁ is regulated by at least twospecific factors, namely by the regulators R₁ ^(a) and R₁ ^(b), whereinR₁ ^(a) can for example be a repressor and R₁ ^(b) can for example be anactivator. This applies analogously to P₂ and R₂ or R₂ ^(a) and R₂ ^(b).

In a preferred embodiment (a) the promoter P₁ and/or the promoter P₂requires that, for binding of the RNA polymerase to the correspondingrecognition sequence of the promoter, a regulator R₁ or R₂ is bound tothe promoter, i.e. transcription takes place provided there is bindingof R₁ to P₁ or of R₂ to P₂.

In another preferred embodiment (b) the promoter P₁ and/or the promoterP₂ requires that, for binding of the RNA polymerase to the correspondingrecognition sequence of the promoter, a regulator R₁ or R₂ is not boundto the promoter, i.e. transcription takes place provided there is nobinding of R₁ to P₁ or of R₂ to P₂. An example of such interaction ofpromoter and regulator is the interaction of a T7 promoter extended byat least one lacO operator sequence in combination with the repressorLacI.

In another embodiment (c) the promoter P₁ and/or the promoter P₂requires that, for binding of the RNA polymerase to the correspondingrecognition sequence of the promoter, a regulator R₁ or R₂ is bound tothe promoter, but the regulator R₁ or R₂ can assume variousconformations, without thereby permanently removing the binding to thepromoter, and transcription then only takes place provided R₁ or R₂ isin one of the possible conformations. An example of said interaction ofpromoter and regulator is the interaction of the ara promoter with itsactivator/repressor AraC.

Preferably the promoters P₁ and P₂ belong to different of theseembodiments (a), (b) and (c), especially preferably (a) and (c).

Preferably the system P₁/R₁ and/or the system P₂/R₂ is influenced byanother element I₁/I₂ (inductors) or a change of the externalconditions. These inductors I₁ or I₂ can for example be biomolecules,which are synthesized by the host, or natural or artificial molecules,which are added from outside. In particular a temperature change mayalso be considered as a change of the external conditions.

Especially preferably I₁ is an inductor for P₁, but not for P₂, and/orI₂ is an inductor for P₂, but not for P₁.

In a preferred embodiment promoter P₁ and/or promoter P₂ comprises, inaddition to the binding site for the RNA polymerase, at least oneenhancer sequence located outside of this binding site and/or at leastone operator sequence.

Enhancers are typically localized in the 3′-untranslated region of thesequence to be expressed. These enhancer sequences can be of prokaryoticor eukaryotic origin. They can be variants of these sequences or can besynthetic enhancer sequences.

In one embodiment the enhancer sequence is the wild-type enhancersequence of the selected promoter.

Preferably P₁ and P₂ comprise in each case independently of one anotherat most 1000 bp, preferably at most 900 bp and especially preferably atmost 800 bp. The presence/embodiment of the Shine-Dalgarno sequence alsohas an influence on the expression rate in prokaryotic hosts. Theconsensus sequence of the Shine-Dalgarno sequence in E. coli is AGGAGG.In a preferred embodiment, in connection with promoter P₁, aShine-Dalgarno sequence is used that coincides in at least 4nucleotides, preferably at least 5 nucleotides, more preferably 6nucleotides, and most preferably completely with the consensus sequence.

In a preferred embodiment, in connection with promoter P₂, aShine-Dalgarno sequence is used that coincides in at least 4nucleotides, preferably at least 5 nucleotides, more preferably 6nucleotides, and most preferably completely with the consensus sequence.

The Kozak sequence has a similar influence on the expression rate ineukaryotic hosts. The Kozak sequence for mammals for example has theconsensus sequence (GCC)GCCR-CCAUGG (<SEQ. ID. NO: 3>), wherein R is apurine, which is located 3 bp upstream of the start codon AUG andwherein a guanine is located downstream of the start codon and the Kozaksequence of yeasts has for example the consensus sequence(A/U)A(A/C)AA(A/C)AUGUC(U/C) (<SEQ. ID. NO: 4>).

In one preferred embodiment the consensus sequence is used in connectionwith promoter P₁ in a eukaryotic host.

In another preferred embodiment the consensus sequence is used inconnection with promoter P₂ in a eukaryotic host.

In yet another preferred embodiment, on the empty expression vectoraccording to the invention, neither a Shine-Dalgarno sequence nor aKozak sequence is arranged on the insertion sequence in both readingdirections. This preferred embodiment relates to the expression vectorin the original state, i.e. in the state in which no DNA to be expressedor other DNA has been cloned into the insertion sequence (e.g. thepolylinker). Such a vector is also known as “empty vector” by a personskilled in the art. In this embodiment of the expression vectoraccording to the invention, the sequence to be cloned into the insertionsequence then preferably comprises a Shine-Dalgarno sequence or a Kozaksequence.

The in vivo promoter strength is defined by the RNA synthesis rate thatis triggered by a single promoter sequence, and leads to a correspondingproportion of the desired target protein in the total protein content ofthe host organism. The promoters used lead to a content of an expressedtarget protein relative to the total protein content of preferably >1%,preferably >5%, more preferably >10%, and most preferably >25%, inparticular >50%.

The two promoters P₁ and P₂ converge together according to theinvention, i.e. they are convergent, face-to-face. Convergent promotersare produced by arranging promoter P₁ on one DNA strand and promoter P₂on the complementary DNA strand of the expression vector. In otherwords, according to the invention, promoter P₁ and the sequencecomplementary to promoter P₂ are arranged on one DNA strand and promoterP₂ and the sequence complementary to promoter P₁ are arranged on thecomplementary DNA strand of the expression vector.

Convergent promoters are to be distinguished from bidirectionalpromoters, even though the two terms are occasionally used synonymouslyin the literature.

In its true sense, a bidirectional promoter denotes a promoter region ortwo back-to-back cloned promoters, whose reading directions point awayfrom each other, and with which two open reading frames flanking thepromoter region are read. Such promoters are widely distributed, as theycan be used in the coexpression of a reporter gene present instoichiometric ratio to the target gene, in particular in cell cultures.In this connection, reference may be made for example to Sammarco etal., Anal. Biochem. 2005, 346(2), 210-216; Baron et al. Nucleic AcidsRes. 1995, 23(17), 3605-6; and EP-A 1 616 012.

In contrast, convergent promoters, such as the promoters P₁ and P₂according to the invention, are two face-to-face cloned promoters, whosereading directions point toward each other. Owing to the circularstructure of plasmids and other expression vectors in circular form,bidirectional promoters can also be oriented face-to-face in some way,although not relative to the insertion sequence, which according to theinvention is preferably arranged between the two promoters P₁ and P₂ ineach case downstream, so that the two promoters P₁ and P₂ flank theinsertion sequence on both sides. In this way, by means of the promotersit is possible to control the expression of DNA sequences, which havepreviously been cloned into the region of the insertion sequence, andnamely in both directions of reading.

According to the invention, therefore preferably an insertion sequenceis arranged between P₁ and P₂, in each case downstream, so that theexpression of a DNA sequence cloned into the insertion sequence isplaced under the control of P₁ and P₂. In other words P₁ and P₂ run bothtowards each other, and towards the insertion sequence.

Such insertion sequences are known by a person skilled in the art.Preferably said insertion sequence is a polylinker.

For the purpose of this description, a polylinker (also known by aperson skilled in the art as multiple cloning site (MCS)) means a DNAsegment in a vector, whose sequence contains various cleavage sites forrestriction endonucleases following closely one after another. Thismakes flexible cloning possible, as the one that is most suitable ineach case can be selected and used from the various restriction cleavagesites. The cleavage sites are in this case unique on the vector.

In one preferred embodiment, the polylinker comprises at least 1,preferably at least 2 or at least 3, more preferably at least 4 or atleast 5, and most preferably at least 6 or at least 7 and in particularat least 8 or at least 9 recognition sequences for restrictionendonucleases, which optionally overlap. In this connection, therestriction endonucleases are preferably restriction endonucleases oftype I, II or III, which are listed in the REBASE database(http://rebase.neb.com/rebase). Furthermore, in this connection,recognition sequences for restriction endonucleases are to be understoodpreferably as penta-, hexa-, hepta- or octamers preferably of adouble-stranded DNA sequence. Preferably the hexa- or octamers arepalindromic, i.e. on both strands in one direction (for example 5′-3′)they show the same base sequence, e.g. GAATTC or GCGGCCGC. In anotherpreferred embodiment these recognition sequences are interrupted, i.e.between parts of the fixed recognition sequences there are freelyselectable sequences, e.g. CACNNNNGTG (SEQ ID No. 5) or GCNNGC.

In yet another preferred embodiment the polylinker comprises a sequencesegment of at most 20 bp, preferably of at most 15 bp, on which thereare at least 1 or at least 2, preferably at least 3 or at least 4, morepreferably at least 5 or at least 6, and most preferably at least 7 orat least 8, and in particular at least 9 or at least 10 cleavage sitesof restriction endonucleases, which optionally can overlap. In thisconnection, restriction endonucleases are preferably to be understood asrestriction endonucleases of type I, II or III, which are listed in theREBASE database (http://rebase.neb.com/rebase).

In addition to restriction endonucleases, basically homing endonucleasescan also be considered.

In one preferred embodiment, between the last by of promoter P₁ and thelast by of promoter P₂, an insertion sequence is arranged inface-to-face arrangement, which comprises at most 500 bp, preferably atmost 200 bp, more preferably at most 100 bp, more preferably at most 50bp, and most preferably at most 20 bp and in particular at most 6 bp. Inthis connection the expression “last bp” refers to the reading directionof the RNA polymerase. This preferred embodiment relates to theexpression vector in the original state, i.e. in that state in which noDNA to be expressed or other DNA has yet been cloned into the insertionsequence (e.g. the polylinker) (empty vector).

In an especially preferred embodiment, on the insertion sequence thereare at most 100, preferably at most 50, preferably at most 20,preferably at most 10 cleavage sites, preferably at most 5 cleavagesites and especially preferably at most 1 cleavage site of restrictionendonucleases, which preferably have a recognition sequence between 4and 10 b and produce overhanging or smooth ends. Especially preferably,the restriction endonucleases are selected from the group comprisingAanI (PsiI), AarI, AasI (DrdI), AatII, Acc65I (KpnI), AdeI (DraIII),AjiI (BmGBI), AjuI, AlfI, AloI, AluI, Alw21I (BsiHKAI), Alw26I (BsmAI),Alw44I (ApaLI), ApaI, BamHI, BauI (BssSI), BclI, BcnI (NciI), BcuI(SpeI), BdaI, BfiI (BmrI), BfmI (SfcI), BfuI (BciVI), BglI, BglII,Bme1390I ScrFI), BoxI (PshAI), BpiI (BbsI), BplI, Bpu10I, Bpu1102I(BlpI), BseDI (BsaJI), BseGI (FokI), BseJI (BsaBI), BseLI (BslI), BseMI(BsrDI), BseMII (BspCNI), BseNI (BsrI), BseSI Bme1580I), BseXI (BbvI),Bsh1236I (BstUI), Bsh1285I (BsiEI), BshNI (BanI), BshTI (AgeI), Bsp68I(NruI), Bsp119I (BstBI), Bsp120I (PspOMI), Bsp143I (Sau3AI), Bsp1407I(BsrGI), BspLI (NlaIV), BspOI (BmtI), BspPI (AlwI), BspTI (AflII),BsT1107I (BstZ17I), BstXI, Bsu15I ClaI), BsuRI (HaeIII), BveI (BspMI),CaiI (AlwNI), CfrI (EaeI), Cfr9I (XmaI), Cfr10I (BsrFI), Cfr13I(Sau96I), Cfr42I (SacII), CpoI (RsrII), CseI (HgaI), Csp6I (CviQI),DpnI, DraI, Eam1104I (EarI), Eam1105I (AhdI), Eci136II (EcoICRI), Eco24I(BanII), Eco31I (BsaI), Eco32I (EcoRV), Eco47I (Avail), Eco47III (AfeI),Eco52I (EagI), Eco57I (AcuI), Eco57MI, Eco72I (PmlI), Eco81I (Bsu36I),Eco88I (AvaI), Eco91I (BstEII), Eco105I (SnaBI), Eco130I (StyI), Eco147I(StuI), EcoO109I (DraII), EcoRI, EcoRII, EheI (NarI), Esp3I (BsmBI),FaqI (BsmFI), FspAI, FspBI (Bfai), GsuI (BpmI), HhaI, Hin1I (AcyI),Hin1II (NlaIII), Hin4I, Hin6I (HinP1I), HincII (HindII), HindIII, HinfI,HpaII, HphI, Hpy8I (MjaIV), HpyF3I (DdeI), HpyF10VI (MwoI), KpnI, Kpn2I(BspEI), KspAI (HpaI), LguI (SapI), Lsp1109I (BbvI), LweI (SfaNI), MauBIMbiI (BsrBI), MboI, MboII, MlsI (MscI), MluI, MnlI, Mph1103I (NsiI),MreI (Sse232I), MspI (HpaII), MssI (PmeI), MunI (MfeI), MvaI (BstNI),Mva1269I (BsmI), NcoI, NdeI, NheI, NmuCI (Tsp45I), NotI, NsbI (FspI),OliI (AleI), PaeI (SphI), PagI (BspHI), PasI, PauI (BssHII), PdiI(NaeI), PdmI (XmnI), PfeI (TfiI), Pfl23II (BsiWI), PfoI, PpiI, Ppu21I(BsaAI), PscI (PciI), Psp5II (PpuMI), Psp1406I (AclI), PstI, PsuI(BstYI), PsyI (Tth111I), PvuI, PvuII, RsaI, RsaI (MsII), SacI, SalI,SatI (Fnu4HI), ScaI, SI (PleI), SdaI (SbfI), SduI (Bsp1286I), SfaAI(AsISI), SphiI, SgrDI, SgsI (AscI), SmaI, SmiI (Swal), SmoI (SmlI), SmuI(FauI), SsiI (AcyI), SspI, TaaI (HpyCH4III), TaiI (MaeII), TaqI, TasI(Tsp509I), TatI, TauI, Tru1I (MseI), TscAI (TspRI), TsoI, TstI, Van91I(PfIMI), VspI (AseI), XagI (EcoNI), XapI (ApoI), XbaI, XceI (NspI),XhoI, XmaJI (AvrII) and XmiI (AccI).

Especially preferably the insertion sequence comprises at most 50 bp andhas at least 6 cleavage sites for restriction endonucleases.

To ensure a translation in all three reading frames, in a preferredembodiment according to the invention a system of expression vectors isalso comprised, in which the whole sequence or parts of the sequence ofthe polylinker are in each case displaced by one nucleotide with respectto the rest of the vector sequence. For illustration of this teaching,reference should be made to the works of Charnay et al. (1978) Nucl.Acid Res. 5: 4479 and Villa-Komaroff (1978) Proc. Natl. Acad. Sci. 75,3727.

In another preferred embodiment the empty expression vector according tothe invention does not comprise a translation start, i.e. there is alsono start codon ATG or GTG within the insertion sequence in bothdirections of reading. In this preferred embodiment, the sequence to becloned into the insertion sequence then preferably contains saidtranslation start including a start codon.

In one preferred embodiment, there is no ribosome binding site on theinsertion sequence in both directions of reading. It is thereby ensuredthat translation of the resultant mRNA cannot be initiated by the emptyvector of the two promoters. Especially preferably the empty expressionvector according to the invention contains neither ribosome bindingsites nor start codons in the insertion sequence in both directions ofreading.

In an especially preferred embodiment, on the insertion sequence thereis (still) no gene, e.g. for a particular antibiotic resistance, so thatthe empty expression vector only contains the insertion sequence as suchbetween P₁ and P₂. In this way it is ensured that both promoters relatefunctionally to the insertion sequence, i.e. to both DNA strands of theinsertion sequence, so that cloning into the insertion sequence can takeplace undirected. In this connection, “undirected” means that accordingto the invention, ultimately it does not matter into which of the twoDNA strands of the plasmid a particular sequence is inserted, as bothpromoters relate functionally to the insertion sequence, the insertedsequence is inevitably placed either under the control of P₁ or underthe control of P₂. Expression of the inserted sequence is thus ensuredin each case.

Conversely, if in the empty expression vector a gene were already to beplaced under the control of e.g. P₁, for example a gene for a particularantibiotic resistance, undirected cloning would not be possible (or atleast would be associated with disadvantages), as a (further) insertiondownstream of P₁ would always result in coupling of expression of theinserted sequence with the gene already present. For the case when thegene for antibiotic resistance is followed by a terminator, the insertedforeign DNA, which would be inserted after the gene, would only be underthe control of the relevant promoter to a limited extent, or not at all,and the advantage according to the invention, of two promoters directedon the same insertion sequence, would be lost.

Decoupling of expression of the inserted sequence from the gene that isunder the control of P₁ would however necessitate a directed cloninginto the insertion sequence downstream of P₂, i.e. specifically into theother DNA strand. However, directed clonings require a corresponding5′-3′-orientation of the sequence to be inserted, so that by means ofsuch an expression vector ultimately it would still only be possible toscreen 50% of a DNA variant library.

In an alternative embodiment, the expression vector according to theinvention can contain as insertion sequence, instead of or additionallyto a polylinker, also a sequence that permits integration of DNAsequences by recombination.

Methods for integrating DNA sequences into a vector, preferably anexpression vector, are known by a person skilled in the art. Forexample, such a method is based on recombination via att-sites, as forexample in the GATEWAY vectors of the company Invitrogen (Carlsbad,Calif., USA). Another method is described in Muyrers J. P. P, Zhang Y.,and Stewart A. F. (2001) “Recombinogenic engineering—new options forcloning and manipulating DNA” TIBS 26: 325-331. The DNA to be cloned a(meta-)genome bank would then have to be pretreated with correspondinglinkers. Methods for attaching linkers to DNA are known by personsskilled in the art.

In one preferred embodiment, a secretion sequence that has the purposethat, after expression, the host secretes the expressed peptide orprotein, is arranged after the last by of P₁ and/or after the last by ofP₂, but before the polylinker. For this, it is necessary that there isno stop codon between the secretion sequence and the polylinker. Thenthe cloned DNA sequences are preferably searched for sequences thatproduce, as a result of cloning, a fusion protein of signal peptide andencoded protein. Suitable secretion sequences are biologically definedand are known by a person skilled in the art.

In another preferred embodiment, in addition to the polylinker and/orDNA sequences for recombination, the insertion sequence also comprises aso-called suicide sequence. Suicide sequences are sequences that lead todying-off of certain hosts. For example, the suicide sequence codes fora restriction endonuclease (e.g. EcoRI), which through digestion of thegenomic DNA leads to dying-off of hosts that do not encode an associatedmethyltransferase (e.g. EcoMI) which protects the own DNA. The cleavagesites of the polylinker are in this case arranged within the suicidesequence. If additional DNA sequences are now cloned into thepolylinker, the suicide gene is interrupted and becomes inactive. Thisprevents the formation of so-called religands, i.e. vectors that arereligated again without additional DNA, during cloning of the DNA andsubsequent transformation of the vectors into suitable hosts. In thiscase, the expression vector according to the invention is preferablyproduced in a host that expresses the corresponding protectivemethyltransferase, whereas the banks are then constructed in a host thatdoes not encode the protective methyltransferase. A great variety ofother suicide systems are known by a person skilled in the art. Forexample, reference may be made to the pJET system from the companyFermentas (Vilnius, Lithuania); Quandt J and Hynes M F (1993) “Versatilesuicide vectors which allow direct selection for gene replacement ingram-negative bacteria”, Gene 127, 15-21; Ortiz-Martin et al., (2006)“Suicide vectors for antibiotic marker exchange and rapid generation ofmultiple knockout mutants by allelic exchange in Gram-negativebacteria”, J Microbiol Methods. 67, 395-407; Schlieper et al., (1998) “APositive Selection Vector for Cloning of Long Polymerase Chain ReactionFragments Based on a Lethal Mutant of the crp Gene of Escherichia coli”,Anal. Biochem. 257, 203-209 or Bej et al., (1988) “Model suicide vectorfor containment of genetically engineered microorganisms.”, Appl EnvironMicrobiol. 54, 2472-7.

Convergent promoters are known from the prior art. Thus, in somecommercial cloning plasmids there are two convergent promoters on eitherside of the polylinker (multiple cloning site, MCS), e.g. T7 and SP6promoter in pDrive (Merck, Darmstadt). However, these cloning plasmidsare not expression plasmids, as they do not serve for functionalexpression of the cloned genes in vivo, but only for generating RNA byin-vitro transcription, e.g. for Northern blots, and as primer sitesthat are often used for sequencing. Moreover, the convergent promotersare not independently inducible on these cloning vectors. Convergentpromoters are also described for plasmids, with which sense andantisense RNA is said to be produced simultaneously, to obtain siRNA anddsRNA for gene silencing in eukaryotes (cf. e.g. Waterhouse et al.,Plant Biology, 1998, 95, 13959-64; Zheng et al., PNAS, 2004, 101,135-40. Convergent promoters also occur naturally in bacteria, e.g. inBacillus, where two promoters effect the reading of two different geneproducts on the sense and antisense strand of the same DNA segment (Wanget al., J. Bacteriol., 1999, 181, 353-6).

The use of a vector with two convergent promoters for screening a(meta)genome library is also described in the literature (cf. Lammle etal., Journal of Biotechnology, 2007, 127, 575-92). This is the vectorpJOE930 (Altenbuchner et al., Methods Enzymol., 1992, 216, 457-66),which bears two convergent, comparatively weak lac promoters and can beused for the cloning and IPTG-induced expression of metagenomic DNA. Thepalindromic sequence of the two lac promoters and the MCS enclosed bythem cause instability of the empty vector in E. coli. Furthermore,owing to their similarity, the two promoters are not separatelyinducible.

It was found, surprisingly, that separately inducible convergentpromoters have advantages over convergent promoters that are notseparately inducible.

For the purpose of this description, separate inducibility of thepromoters P₁ and P₂ means that promoter P₁ can be induced selectively bysuitable measures, without promoter P₂ also being induced simultaneouslyto a significant extent, and vice versa. Preferably, in selectiveinduction of promoter P₁, promoter P₂ is induced by at most 10% of itsmaximum inducibility, preferably at most 1%, more preferably at most0.5%, and most preferably at most 0.2% and in particular at most 0.1%,and vice versa. Separate inducibility of the promoters can be achievedin the simplest case by using promoters P₁ and P₂ that interact withdifferent modulators (repressors, activators).

The empty expression vector according to the invention has, without theinsertion sequence, altogether at most 3000 bp, i.e. the completesequence of the expression vector including P₁ and P₂ but excluding theinsertion sequence comprises at most 3000 bp.

In a preferred embodiment, the empty expression vector according to theinvention comprises, after opening in the insertion sequence or aftercutting out parts of the insertion sequence that are not required,altogether at most 3000 bp, preferably at most 2900 bp, preferably atmost 2800 bp, preferably at most 2700 bp, more preferably at most 2600bp, and most preferably at most 2550 bp and in particular at most 2500bp.

In another preferred embodiment the empty expression vector according tothe invention as such comprises altogether at most 3000 bp, preferablyat most 2900 bp, preferably at most 2800 bp, preferably at most 2700 bp,more preferably at most 2600 bp, and most preferably at most 2550 bp andin particular at most 2500 bp.

In yet another preferred embodiment the empty expression vectoraccording to the invention, without insertion sequence, comprisesaltogether at most 2900 bp, preferably at most 2800 bp, preferably atmost 2700 bp, more preferably at most 2600 bp, and most preferably atmost 2550 bp and in particular at most 2500 bp.

Preferably the expression vector according to the invention does notcode for a regulator of P₁ and/or a regulator of P₂.

In a preferred embodiment of the expression vector according to theinvention, P₁ is a T7 promoter. The T7 promoter is known by a personskilled in the art. In this connection, for example reference may bemade in its entirety to Studier and Moffatt (1986) “Use of bacteriophageT7 RNA polymerase to direct selective high-level expression of clonedgenes” J Mol Biol 189, 113-130. The term “T7 promoter” denotes, in thesense of the present invention, a promoter that is recognized astranscription start by the T7-RNA polymerase and that has been expandedby at least one lacO operator sequence. LacI is then the repressor ofthe T7 promoter.

In a preferred embodiment of the expression vector according to theinvention, P₂ is a promoter that is regulated by arabinose (I₂), inparticular the ara promoter. In a preferred embodiment it is an arapromoter from Gram-negative bacteria, preferably E. coli. In this casethe expression vector according to the invention preferably does notcode for the regulator AraC of the ara promoter.

The ara promoter is known by a person skilled in the art. The arabinoseoperon consists of a controllable promoter region (ara promoter), andthree structural genes (araB, araA and araD), which code for proteinsfor degradation of L-arabinose. AraC is expressed constitutively. Thegene product serves as a repressor. It binds to the promoter and thusprevents transcription of the genes araB, araA and araD. If arabinose ispresent, it binds to AraC. As a result of arabinose being bound, AraCchanges its shape, binds to other DNA sequences and thus becomes theactivator. Therefore the RNA polymerase can now attach to the promoter,and transcription of the structural genes begins. When the arabinose hasdegraded completely, AraC changes conformation again and transcriptionstops again. For further details, reference may be made for example toSchleif R. (2000) Regulation of the L-arabinose operon of Escherichiacoli. Trends Genet. 16, 559-65 in its entirety.

In another preferred embodiment the expression vector according to theinvention is characterized in that it codes in each case for at leastone terminator T₁ or T₂ in the corresponding direction of reading of thepromoters P₁ or P₂.

In a preferred embodiment of this, the expression vector has thefollowing arrangement of P₁, P₂, T₁, T₂ and of the insertion sequence:T₂ (antisense)-P₁ (sense)-insertion sequence (sense/antisense)-P₂(antisense)-T₁ (sense).

Especially preferably, T₁ is a T7-terminator. Especially preferably, T₂is a terminator for the host RNA polymerase.

In a preferred embodiment the terminator for the T7 promoter is theT7-terminator and the terminator for the ara promoter is a terminatorsequence for the E. coli RNA polymerase. In an especially preferredembodiment no independent terminator is cloned for the ara promoter,instead the terminator of the gene of the expression vector locatedupstream cloned in antisense is used.

Within the scope of the present invention, “T_(i)” denotes optionally T₁or T₂.

In another especially preferred embodiment the expression vector ischaracterized in that an additional gene is located between P_(i) andits terminator T_(i) in the direction of reading of P_(i) but after thesecond promoter P_(j).

Furthermore, the expression vector according to the invention comprisesa selection marker sequence, which is suitable for distinguishing hoststhat contain the expression vector, from hosts that do not contain theexpression vector.

This can for example be achieved by the selection marker sequenceendowing the host with antibiotic resistance, so that it is capable ofsurviving on nutrient media on which other hosts, which do not containthe expression vector, die. Suitable sequences that impart antibioticresistance are known by a person skilled in the art. The antibioticagainst which resistance is imparted by the selection marker sequence ispreferably selected from the group comprising ampicillin, tetracycline,kanamycin, chloramphenicol, spectinomycin, hygromycin, sulphonamide,trimethoprim, bleomycin/phleomycin, Zeocin™, gentamicin and blasticidin.

Alternatively, auxotrophic hosts (negative mutants) can be used, whichare dependent on a particular nutrient for survival (amino acid,carbohydrate, etc.), which they cannot synthesize themselves. Thesehosts are then not capable of surviving on a nutrient medium that doesnot supply this nutrient. In this case the selection marker sequence onthe expression vector according to the invention endows the host withthe ability to synthesize this nutrient, so that capability of survivingon the deficient nutrient medium is induced by the expression vector.Suitable selection marker sequences are known by a person skilled in theart.

In the case of yeast cells, the markers used can be those that enableauxotrophic yeast strains to grow without additional uracil, tryptophan,histidine, leucine or lysine in the medium.

In the case of mammalian cells, the markers used can be for examplesequences that code for the activity of DHFR, of cytosine-deaminase, ofhygromycin-β-phosphotransferase (HPH), of puromycin-N-acetyl transferase(PAC), of thymidine kinase (TK) and of xanthine-guaninephosphoriboseultransferase (XGPRT).

Alternatively, sequences can be used that code for a counterselectionmarker, for example the sacB gene of B. subtilis or the F-plasmidccdB-gene or colicin-release-gene such as the kil-gene for colicinE1.

Another example is the use of a fragment of the Mu phage as described inSchumann (1979) Mol. Gen. Genet. 174, 221-4. Other examples of suchmarkers are described in Roberts et al. (1980) Gene 12, 123-7; Dean(1981) Gene 15, 99-102, Hennecke et al. (1982) Gene 19, 231-4 orHashimoto-Gotoh et al. (1986) Gene 41, 125-8.

Additionally, sequences can be used that permit selection on the basisof the blue/white coloration after adding IPTG/X-GAL.

Additionally sequences can be inserted in the region between promotersP₁ and P₂, which make screening by PCR possible.

In one embodiment, expression vectors can be used that permitcoexpression of the cloned sequence with a detectable marker. Saiddetectable marker can for example be a tag such as a His tag, a Poly-Histag, an MAT tag, a streptavidin tag, a streptavidin-binding tag, a GSTtag, an antibody-binding tag, a Myc tag, a Swa11 epitope or a FLAG tag.In one embodiment they can also be fluorescent tags such as a GFP tag, aBFP tag or an RFP tag.

In a preferred embodiment the expression vector according to theinvention has at least 70%, preferably at least 80%, more preferably atleast 85%, and most preferably at least 90% and in particular at least95% homology to <SEQ ID NO: 1>. Homology is preferably determined usingthe algorithm according to Smith & Waterman (J Mol Biol., 1981, 147(1),195-7), using the BLOSUM62 matrix and values of 11.0 for the opening ofa gap, or 1.0 for the widening of a gap.

Another aspect of the invention relates to an expression systemcomprising the expression vector described above and separatelyoccurring regulatory sequences, which code for a regulator R₁ of P₁and/or for a regulator R₂ of P₂. In this connection, “separately” meansthat the regulatory sequences are not located on the expression vectoraccording to the invention, or one or more parts integrated into thehost chromosome. Preferably the regulatory sequences are located on avector (regulatory vector), which codes for a regulator R₁ of P₁ and/orfor a regulator R₂ of P₂. Preferably R₁ is LacI and/or R₂ is AraC.

The regulatory vector according to the invention preferably codes forboth regulators R₁ and R₂ of the two promoters P₁ and P₂, which arelocated on the expression vector according to the invention.

Possible regulatory vectors include, for example, plasmids, phage,cosmids, phasmids, fosmids, bacterial artificial chromosomes, yeastartificial chromosomes, viruses and retroviruses (for example vaccinia,adenovirus, adeno-associated virus, lentivirus, herpes-simplex virus,Epstein-Barr virus, fowlpox virus, pseudorabies, baculovirus) andvectors derived therefrom.

The regulatory vector or parts thereof can also be integrated into thegenome.

Any other vector can be used for production of the regulatory vectoraccording to the invention, provided it is replicable and capable ofsurviving in the selected system (host).

Preferably the regulatory vector is a plasmid (called “regulatoryplasmid” within the scope of the invention).

Preferably the expression vector according to the invention is also aplasmid, so that the expression system according to the inventionpreferably comprises two plasmids: expression plasmid and regulatoryplasmid.

In a preferred embodiment the regulatory plasmid comprises more by thanthe expression vector or the expression plasmid.

In one preferred embodiment the regulatory plasmid according to theinvention is a low-copy plasmid (on average <100 plasmids per cell). Inanother preferred embodiment the regulatory plasmid according to theinvention is a high-copy plasmid (on average ≥100 plasmids per cell).

The regulatory vector also contains a selection marker sequence.Preferably the selection marker sequence of the regulatory vector isdifferent from the selection marker sequence of the expression vector.

The regulatory vector preferably serves for effective control both of P₁and of P₂. It is then the ara promoter and the T7 promoter, thereforethe regulatory vector is preferably a vector expanded by anaraC-variation and a part of the ara-regulatory region, whichadditionally bears the structural gene for the LacI repressor.

AraC is the repressor/activator of the ara promoter, and LacI is therepressor of the T7 promoter.

The LacI repressor performs two functions. On the one hand it binds toregulatory elements between T7 promoter and transcription start(operator sequence lacO) and prevents the start of transcription. On theother hand, in a preferred embodiment, expression of the T7-RNApolymerase in the expression host is also under the control of a lacOoperator sequence. For as long as the LacI repressor is bound to thisoperator sequence, expression of the T7-RNA polymerase itself issuppressed and therefore also does not transcribe any sequences that areunder the control of the T7 promoter. IPTG (I₁) binds to the ladrepressor, which is inactivated as a result and can no longer bind tothe operator sequences lacO and so transcription of the T7-RNApolymerase itself, and of the genes located downstream of the T7promoter is released.

This permits effective control of expression by IPTG- orL-arabinose-induction (inductor I₁ or inductor I₂). The expressionvector according to the invention preferably comprises as cloning orexpression component of the 2-component system on one side of the MCS,the T7-promoter/operator region, and on the other side the completeAra-promoter-operator region (cf. FIG. 1).

In the literature, the ara-regulator AraC is generally expressed on thesame plasmid as the target gene. This is preferably not so with theexpression vector according to the invention. In this way a plasmid isobtained that is reduced in size to the maximum, which offers advantagesin the bottleneck of ligation/transformation, as the achievabletransformation rates and hence achievable library sizes are larger, thesmaller the plasmid used. Instead, araC can be cloned into theT7-regulatory plasmid, where, like lacI, it is expressed independentlyof the expression plasmid. At the same time, the araC gene is preferablyshortened, to ensure more efficient inductor binding. (Lee et al.,(2007); Appl. Environ. Microbiol. 73, 5711-5715).

In a special embodiment the regulatory vector bears additionally atleast one gene for a transfer-RNA of the host organism. Preferably thesegenes are selected from the group comprising argU, argW, ileX, gluT,leuW, proL, metT, thrT, tyrU, thrU and argX of E. coli, which recognizethe codons AGG, AGA, AUA, CUA, CCC, GGA or CGG. Through the presence ofthese additional transfer-RNA genes, target genes that have a usage ofthe amino acid codons in their sequence different from E. coli (codonusage) can also be expressed at higher yield by the expression vector.This can occur in particular for eukaryotic genes (e.g. human) or genesfrom other groups of microorganisms (e.g. actinomycetes).

In another special embodiment the regulatory vector contains genes forone or more inhibitory proteins for one or more RNA polymerases. Theseone or more RNA polymerases are the RNA polymerase(s) that are used,i.e. the RNA polymerase of the host and/or an RNA polymerase foreign tothe host, coexpressed in the host cell.

In yet another special embodiment, the expression system, preferably theregulatory vector, contains the gene lysS, which codes for theT7-lysozyme. The T7-lysozyme can bind to the T7-RNA polymerase andinactivate it. Through the presence of this gene in the host cell, basalexpression of T7-RNA polymerase is suppressed and expression does nottake place until expression of the T7-RNA polymerase is increased byadding an external inductor (IPTG) and is no longer capable of bindingsufficient T7-lysozyme. In this way, even very toxic proteins can beexpressed under the control of the T7 promoter. As economicallyimportant enzymes often present hydrolytic and therefore toxicactivities (proteases, lipases etc.) this is of particular advantage.

Expression vector and regulatory plasmid are compatible according to theinvention and can preferably be replicated simultaneously in the host,e.g. in E. coli. Reading of the T7 promoter in E. coli requiresexpression of T7-polymerase, for example as in E. coli BL21(DE3). Theara promoter does not require any E. coli-foreign polymerase.

Preferably the regulatory plasmid according to the invention comprisesaltogether at most 7000 bp, preferably at most 6500 bp, more preferablyat most 6000 bp, and most preferably at most 5500 bp and in particularat most 5000 bp.

Especially preferably the regulatory plasmid according to the inventionhas at least 70% homology to <SEQ ID NO: 2>. The homology is preferablydetermined by the algorithm according to Smith & Waterman (J Mol Biol,1981, 147(1), 195-7), using the BLOSUM62 matrix and values of 11.0 forthe opening of a gap, or 1.0 for the widening of a gap.

Another aspect of the invention relates to a method of expression of DNAsequences using the expression vector or expression system describedabove comprising the steps

-   (i) optionally transfecting or transforming a suitable host organism    with the regulatory plasmid;-   (ii) cloning a DNA sequence or a DNA sequence mixture (library) into    the expression vector between P₁ and P₂;-   (iii) optionally transfecting or transforming the host organism    obtained in (i) with regulatory plasmid with the constructs obtained    in step (ii); and-   (iv) inducing expression of the proteins encoded by the DNA    sequences by adding the inductor I₁ and/or the inductor I₂.

The DNA sequence is preferably a constituent of a (meta)genome library.Genomic DNA sequences, extrachromosomal DNA sequences and cDNA sequencesare included.

In one embodiment the cloning into the expression vector takes place bysubcloning from another vector.

The terms “transfected” or “transformed” in the sense of the inventioncover all methods of introducing nucleic acids into the host, e.g.including infection. The construct can be introduced in various ways,depending on the host used. Introduction of the construct into aprokaryotic host can for example take place by means of transformation,e.g. electroporation, transduction or transfection. Introduction of theconstruct into a eukaryotic host can, depending on the type of construct(expression vector), for example take place via calcium phosphate-DNAcoprecipitation, DEAE-dextran-mediated transfection, polybrene-mediatedtransfection, electroporation, microinjection, liposome fusion,lipofection, viral infection, retroviral infection or ballistic methods.

According to the invention, the regulatory vector or at least the partsthat encode the repressor can also be introduced into the host by thesemethods.

In one preferred embodiment of the method according to the invention, I₁and I₂ are added successively. It was found, surprisingly, that in thisway inhibition of the weaker promoter can be avoided.

In another preferred embodiment of the method according to theinvention, I₁ and I₂ are added to spatially separate partial cultures ofthe organisms obtained and therefore the two promoters are inducedindividually. It was found, surprisingly, that mutual inhibition of thepromoters can also be avoided in this way.

Therefore, according to the invention preferably spatially separateinduction of reading of the same sequence takes place in differentdirections of reading, but not the successive or simultaneous inductionof reading of different sequences.

Especially preferably I₁ is the inductor for P₁, but not for P₂, and/orI₂ is the inductor for P₂, but not for P₁.

Another aspect of the invention relates to a method of screening of DNAlibraries using the expression vector or expression system describedabove comprising the method described above for expression of DNAsequences.

Preferably screening is carried out with respect to catalytic activityof the expressed proteins. Preferably it is catalytic activity of one ofthe following enzyme classes: 1. Oxidoreductases, 2. Transferases, 3.Hydrolases, 4. Lyases, 5. Isomerases and 6. Ligases. Preferredoxidoreductases are selected from the EC group comprising 1.1, 1.2, 1.3,1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 1.10, 1.11, 1.12, 1.13, 1.14, 1.15, 1.16,1.17, 1.18, 1.19 and 1.97. Preferred transferases are selected from theEC group comprising 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8 and 2.9.Preferred hydrolases are selected from the EC group comprising 3.1, 3.2,3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 3.10, 3.11 and 3.12. Preferred lyasesare selected from the EC group comprising 4.1, 4.2, 4.3, 4.4, 4.5, 4.6and 4.99. Preferred isomerases are selected from the EC group comprising5.1, 5.2, 5.3, 5.4, 5.5 and 5.99. Preferred ligases are selected fromthe EC group comprising 6.1, 6.2, 6.3, 6.4 and 6.5. The EC nomenclatureintroduced by the International Union of Biochemistry and MolecularBiology (IUBMB) is known by a person skilled in the art. Informationabout this can be found on the website of the IUBMB.

Suitable assays for detecting a given catalytic activity are known by aperson skilled in the art. They are preferably based on UV/VISspectroscopy, fluorescence, luminescence or radioactivity. In thisconnection, reference may be made for example to J. L. Reymond, EnzymeAssays: High-throughput Screening, Genetic Selection and Fingerprinting,Wiley VCH, 2006 in its entirety.

Alternatively, however, screening based on binding affinities is alsopossible. For example, this can be the binding affinity to an antibodyor to some other binding partner (for example a protein or a nucleicacid or a carbohydrate).

Screening based on functional assays that are suitable in each case, andknown by persons skilled in the art, is also possible.

In one embodiment the selected sequence is identified by sequencing thecloned sequence.

In a special embodiment of the method, the host cell is multiplied andthe expressed protein can be submitted to further steps such aspurification and/or biochemical and/or functional characterization.

In a special embodiment these steps take place using the tags linked tothe expressed protein. As tags, it is possible for example to use a Histag, a Poly-His tag, a MAT tag, a streptavidin tag, astreptavidin-binding tag, a GST tag, an antibody-binding tag, a Myc tag,a Swa11 epitope or a FLAG tag or fluorescent tags such as a GFP tag, aBFP tag or an RFP tag.

The preferred field of application of the expression vector according tothe invention is as cloning and expression vector for the enzymeactivity screening of genome and metagenome libraries. In fact, with(meta)genome libraries, high complexity (>10⁶ clones) is necessary, sothat already when they are being prepared, high cloning andtransformation efficiency is decisive. Furthermore, the ideal screeningvector must also enable efficient screening of large numbers of clones.In cluster screening, as in other screening assays, strong, controllableexpression of the target proteins is essential. The expression vectoraccording to the invention was specially developed for theserequirements—high cloning efficiency combined with efficient,controllable expression.

In contrast to the systems known from the prior art, the expressionvector according to the invention has two strong, plasmid-locatedpromoters, which moreover are still controllable, which offersadvantages in screening for slightly toxic proteins. In the case ofslightly toxic proteins, in fact, the host organism, e.g. E. coli,tolerates the presence of these proteins only for a relatively shorttime. In such cases, controllable promoters make it possible for thegene that codes for these slightly toxic proteins to be “switched off”at first, until the host organism has multiplied sufficiently. Then thecontrollable promoters enable the gene to be “switched on”, thusinducing production of the slightly toxic proteins for some time, beforethe expressed proteins exert their toxic action. In addition to thepossible toxicity of a target protein, generally every additionalexpression of a recombinant protein represents a stress for the hostorganism (consumption of resources). Therefore as a rule it is alwaysadvantageous to switch on expression of the recombinant proteins onlyafter reaching sufficiently strong multiplication.

With the two convergent promoters in the expression vector according tothe invention, it is possible to cover both potential orientations andthus double the usable information content of the cloned DNA. The ORFscan be expressed independently of orientation and therefore their geneproducts can be screened on the basis of activity.

In addition to the great promoter strength, the separate induction ofthe two promoters is also advantageous, because in this way possibleantisense RNA effects can be excluded.

The separately inducible promoters of the expression vector according tothe invention offer advantages. A decrease in promoter strength, orexpression efficiency of the ORFs read can thus be avoided.

Transcriptional interferences by convergent promoters had already beenobserved with eukaryotes. Thus, Callen et al. describe suppression ofthe weaker promoter by a factor of 5.6 with closely adjacentface-to-face promoters of different strength (Callen et al. (2004),Molecular Cell, 14, 647-56 B). Eszterhas et al. show that with aconvergent promoter arrangement, the activity of two reporter genes isreduced almost to the background level (Eszterhas et al. (2002),Molecular and Cellular Biology 22, 469-79). This is sometimes attributedto disturbance of the binding properties in the promoter region. Theseresults can be transferred to prokaryotes with limitations, taking intoaccount that their transcription initiation differs from that of theeukaryotes.

The expression system according to the invention combines the small sizeof a conventional cloning vector with the expression possibilities ofcontrollable expression vectors. By using the two convergent promoters,the size of library that must be screened in order to cover a certainamount of DNA statistically, is halved. The separate induction of thepromoters prevents possible transcriptional interference by antisenseRNA, which is inevitably formed in simultaneous induction or a reducedtranscription activity of the weaker promoter due to a highertranscription rate of the stronger promoter.

A high, easily controllable promoter strength is of decisive advantagein the cluster screening method, as the strong signals against thebackground are detected better and accordingly greater complexities canbe screened than previously.

Therefore the expression system according to the invention istailor-made for every kind of activity screening of banks withrandomized fragmented (meta)genomic DNA, but in particular for clusterscreening.

This is a method of iterative deconvolution of variant libraries, whichhas considerable advantages over conventional deconvolution methods.

In a preferred embodiment of such a method, shown schematically in FIG.6, a library, preferably a (meta)genome library, is prepared (FIG. 6,Step a.)(i)). The library contains the individual variants “A”, “B”, “C”and “D”. According to the invention, this library is transferred into ahost (FIG. 6, Step a.)(ii)).

In Step b.) the clones of one partial library are divided into a firstcompartment (variants “A” and “B” in FIG. 6) and the clones of anotherpartial library into a second compartment (variants “C” and “D” in FIG.6).

During this dividing-up, it is not known which variants are put in whichcompartment. The compartments can for example be two adjacent wells on afirst microtitre plate (“1st plate”).

Now, in Step c.)(i), multiplication of the clones of the individualpartial libraries takes place, preferably by growth of the organismswithin the compartments on the 1st plate.

In a preferred embodiment, next, in Step c.)(ii), an aliquot of themultiplied organisms is preserved, preferably retaining the compartmentallocation. For retaining the compartment allocation, for example asecond microtitre plate (“2nd plate”) can be used, wherein preferablythe aliquot of the multiplied organisms, which is taken from the firstcompartment on the 1st plate, is transferred to the corresponding firstcompartment on the 2nd plate.

With the unpreserved part of the multiplied organisms, in Step c.)(iii)biomolecules are produced, wherein clones that contain variant “A”produce biomolecules “a”; clones that contain variant “B” producebiomolecules “b”; and so on. Typically, the biomolecules are proteins,which are expressed by the organisms. The host organisms are macerated.A person skilled in the art knows various methods for this, for examplecell lysis with suitable chemicals or cell lysis by osmotic shock or bythe use of shearing forces such as the “French-press” method. The resultis decoupling of phenotype and genotype.

In Step c.)(iv), now in each case all of the biomolecules “a” and “b”contained in the first compartment and all of the biomolecules “c” and“d” contained in the second compartment are tested. This preferablytakes place by screening for a particular biocatalytic activity(phenotype). In the example chosen, only all of the biomoleculescontained in the first compartment “a” and “b” show the desiredbiocatalytic activity, which is shown symbolically with grey shading ofthe first compartment. From the observed phenotype, it is not possibleto draw any direct conclusions about the genotype, as it is notoutwardly apparent which of the biomolecules is responsible for thepositive test, “a” or “b”, and moreover it is not known from whichvariants the totality of the partial library is composed (cf.explanation Step b.) above).

The first compartment therefore contains biomolecules that fulfil thedesired biocatalytic activity, and is selected in Step d.).

The procedure now preferably does not start from the selected partiallibrary in the first compartment as such, but from the preserved partiallibrary in the corresponding first compartment on the 2nd plate(indicated by a dashed line). It is also possible to perform thepreservation of the partial libraries directly in the 1st plate. In Stepe.) the preserved partial library, which comprises the clones ofvariants “A” and “B”, is diluted and divided up. The clones of variants“A” and “B” are transferred respectively to different compartments. Thecompartments can for example be two wells on a third microtitre plate(“3rd plate”).

Finally, in Step f.), Steps c.) to e.) are repeated until in eachcompartment only at most one variant of the gene sequence coding for thebiomolecule is still contained. Under these preconditions, it is thenpossible to draw direct conclusions about the genotype from the observedphenotype, as all biomolecules contained in the compartment go back toan individual, separated clone.

In a special embodiment of the method according to the invention forscreening DNA libraries, the DNA library comprises 10³ to 10²⁵ differentsequences. The DNA library can for example comprise 10³ to 10⁵, 10⁵ to10¹⁰, 10¹⁰ to 10¹⁵, 10¹⁵ to 10²⁰ or even 10²⁰ to 10²⁵ differentsequences.

According to the invention, Steps c.) to e.) can be repeated, and aperson skilled in the art is able, taking into account the size of thelibrary, to determine a number of repetitions appropriate to theparticular circumstances.

According to the invention, Steps c.) to e.) can for example be repeatedat least 1×, preferably at least 2×, preferably at least 3×, morepreferably at least 5×, more preferably at least 10× until individualsequences are individualized.

In a preferred embodiment, after the first division of the library intocompartments of the 1st plate, each compartment contains on average atleast 10, preferably at least 20, more preferably at least 40, and mostpreferably at least 100 and in particular at least 1000 differentvariants. In one embodiment, the partial libraries therefore comprise,in the first round, preferably ≥10, more preferably ≥10², even morepreferably ≥10³ sequences.

The following examples serve for explanation of the invention, but arenot intended to be limiting.

In the following examples, pF2F4 was used, an expression vector for E.coli, in which two strong promoters flank the multiple cloning site (cf.FIG. 1). The promoters are convergent, i.e. their reading directionsconverge towards each other (face-to-face). The promoters that areinducible independently of one another are a T7 promoter and anarabinose promoter. DNA cloned into this vector can thus be transcribedfrom both sides, which halves the number of clones to be screened. Thestrong vector-supported transcription is independent of insert-codedpromoters and thus increases the hit rate.

Example 1

The promoter strength of the ara or T7 promoter in pF2F4 wasinvestigated in various situations using a reporter gene. The data showthat pF2F4, in conjunction with the regulatory plasmid pLacI+ (cf. FIG.2) is optimum for use as the expression plasmid. The reporter gene usedwas an alcohol dehydrogenase (ADH), which was inserted in both possibleorientations. The gene was under the control of the ara promoter or ofthe T7 promoter, respectively. Only the combination of regulatoryplasmid encoded LacI and AraC with the pF2F4 plasmid leads to maximumpossible expression starting from the Ara promoter and from the T7promoter (FIG. 3).

The ara promoter activity is lowered in the BL21 strain withsimultaneous T7 induction to approx. 10% of the initial activity (FIG.4A). The possibility of this effect being based on competitiveinhibition of the regulator AraC by IPTG can be ruled out, as theinhibition is only observed in E. coli BL21(DE3). No significant declinein ara promoter activity is observed in an E. coli strain withoutchromosomal T7-polymerase (DH10B) (FIG. 4B). Here, the T7-activity isswitched off to the greatest extent. The minimal activity stilloccurring is the basal activity of the T7 promoter, which even in E.coli without chromosomal T7-polymerase is recognized to a slight extentby the host organism's own polymerase (FIG. 4).

Example 2—Example of Application of pF2F4: Screening for Esterase/LipaseActivity in a Metagenome Bank

A metagenome library set up in pF2F4 was screened foresterase/lipase-activity, using the cluster screening method(Greiner-Stoeffele, T., Struhalla, M., 2005, WO 2004/002386). The hitrate was compared with that of a metagenome bank cloned into theconventional pUC-vector. The target activity was an activity that isreadily detectable with an established enzyme assay, and whoseoccurrence in metagenome banks has been described sufficiently in theliterature.

1. Preparation of the Metagenome Bank

For the metagenome banks used, metagenomic DNA (mgDNA) was isolated fromthe contents of a sheep's rumen by direct lysis (Zhou. J.; Bruns, M. A.;Tiedje, J. M. (1996): DNA recovery from soils of diverse composition.Appl. Environ. Microbiol; 62(2): 316-22). For preparing the metagenomebank in pF2F4, the mgDNA was then partially digested with therestriction enzyme AluI and ligated by standard methods into the vectorpF2F4, blunt-end cut with Hindi and EcoRV and dephosphorylated(Sambrook, J., Fritsch, E. F., Maniatis, T., (1989). Molecular cloning:A laboratory manual. Cold Spring Laboratory Press 2nd Ed. Cold SpringHarbor, USA).

For preparing the metagenome bank in pUCWhite, a pUC18 derivative, themgDNA was digested with Bsp143I and also ligated by standard methodsinto the vector pUCWhite that had been cut with BamHI anddephosphorylated.

For multiplying the libraries, electrocompetent E. coli DH10B cells weretransformed with the libraries by electroporation. The pF2F4 library hadan average insert size of 3.7 kb with inserts of 2.4-4.6 kb and a sizeof 2.9×10⁶ individual clones. The pUC library had an average insert sizeof 3.5 kb with inserts of 1.9-5.9 kb and a size of 3.9×10⁶ individualclones. After verification of quality, the libraries were isolated bypreparation in the Midi-Scale (Qiagen, Hilden) from E. coli DH10B andelectrocompetent cells of the expression strain E. coli BL21 (DE3) weretransformed with 720 ng (pF2F4-rumen) or 200 ng (pUC-rumen) of thelibrary. The expression strain transformed with the pF2F4 libraryadditionally contained the regulatory plasmid pLacI+.

2. Cell Propagation

Screening of the metagenome banks was performed using the clusterscreening method (Greiner-Stoeffele, T., Struhalla, M., 2005, WO2004/002386). In this high-throughput method, mixed cultures (clusters)of up to 1000 individual clones (here 300) are applied in the initialscreenings. The clusters, to which the hits found in this firstscreening step relate, are diluted and screened again, until singleclone level is reached. The single clones obtained are thencharacterized enzymatically and by methods of molecular biology. In thisexample of application, only the initial screening is carried out. Allpropagations were carried out in conditions optimized for the respectiveexpression system. As the pF2F4 vector possesses two convergent vectors,and these were to be induced separately, from the pF2F4 library, twomain cultures from a preculture were inoculated with standard media.

2.a Preculture

Cultivation of the libraries in the expression strain was carried out inthe 96-well format in deep-well plates. A preculture was grown first.Each well was inoculated with ˜300 individual clones of a metagenomebank, except that well A1 remained uninoculated as a control. At thesame time, aliquots of the inoculated culture medium were plated out inorder to verify the clone number. For the pF2F4-rumen bank, 278individual clones/well were detected and for the pUC-rumen bank 300individual clones/well. Preculture was carried out in 400 μl of medium.During preculture of the pUC library, 1% glucose and 100 μg/mlampicillin were added to the medium. During preculture of the pF2F4library, 0.5% glucose and 50 μg/ml kanamycin and 37 μg/mlchloramphenicol were added to the medium. Propagation took placeovernight at 37° C. and 1000 rpm in a rotary shaker.

2.b Main Culture

For the main culture of the pF2F4 library, two deep-well plates wereinoculated in parallel, as the convergent promoters pAra and pT7 were tobe induced separately. The main cultures of the pUC library and the partof the pF2F4 library to be induced later with IPTG were propagated in1.2 ml of medium with 0.5% glucose and the corresponding antibiotics(ampicillin for the pUC library and kanamycin and chloramphenicol forthe pF2F4 library). The part of the pF2F4 library to be induced witharabinose was propagated in the same medium without glucose. The maincultures were inoculated in each case with 30 μl of preculture, withwell A1 remaining uninoculated as control. After incubation at 30° C.and 1000 rpm, the cultures were induced on reaching an OD of 0.7. Forthis, 1 mM IPTG was added to the pUC library and 0.5 mM IPTG or 0.2%L-arabinose was added to the two pF2F4 plates. Cultivation was continuedovernight at 30° C. and 1000 rpm.

3. Cell Harvesting and Lysis

The expression cultures grown overnight were centrifuged at 4000×g. Theculture supernatant was removed, to be used additionally to the cellextract in the enzyme assay. The cell pellets were digested in CellLyticbuffer to obtain the cell extract. For this, they were each resuspendedin 200 μl CellLytic buffer and incubated for 30 min at 37° C. Then thecell debris was centrifuged at 4000×g for 15 min at 4° C.

CellLytic buffer:

1 ml CellLytic B Cell Lysis Reagent (Sigma-Aldrich, Steinheim)

1 mg lysozyme (Applichem, Darmstadt)

1 μl benzonase (Sigma-Aldrich)

to 10 ml 50 mM K-phosphate buffer pH 8.

4. Enzyme Activity Assay

The activity assays were carried out with pNP-caprylate, an artificialsubstrate, for which a fatty acid consisting of 8 carbon atoms isderivativized via an ester bond with para-nitrophenol. Duringdegradation, p-nitrophenolate is released, which can be detected at 405nm. In each case 5 μl of cell extract or 5 μl of culture supernatant wasmixed with 95 μl of assay buffer in flat-bottomed 96-well plates andincubated for up to 12 h at room temperature. If the background valueswere too high, the cell extracts were diluted 1:10 in KP8T buffer. Thenthe absorption at 405 nm was determined in a microplate reader (Infinite200, Tecan, Crailsheim).

Composition of Assay Buffer:

200 μl pNP-caprylate (Sigma-Aldrich)

to 20 ml KP8T buffer

KP8T buffer:

23.5 ml 1 M K2HPO4

1.5 ml 1 M KH2PO4

2.5 ml 20% Triton X-100

to 500.0 ml AquaMP

pH 8.0.

5. Evaluation

Wells were assessed as a hit for which the Z factor was >4, with Zdefined as follows:Z=(absorption increase of the well−average of the absorption increase ofthe whole 96-well plate)/standard deviation of the average of theabsorption increase of the whole 96-well plate.Results

From the pF2F4-rumen library, ˜26400 clones with a total insert size of97.7 Mb were screened for esterase/lipase activity. Both the culturesupernatants and the cell extracts of both induction batches wereexamined. There were 10 non-redundant hits, which corresponds to a hitrate of 1 hit/9.8 Mb. Hits that appeared in several measurements wereonly included once in the overall balance.

From the pUC-rumen library, ˜28500 clones with a total insert size of99.8 Mb were screened for esterase/lipase activity. Both the culturesupernatants and the cell extracts were examined. There was 1 hit, whichcorresponds to a hit rate of 1 hit/99.8 Mb. Therefore, for themetagenome library in pF2F4 there is a ˜10 times higher hit rate thanfor the pUC library. The hits are summarized in Table 1, and FIG. 5shows the hit distribution in the cell lysis of the pF2F4 libraryinduced with IPTG.

TABLE 1 Esterase/lipase hits in the libraries after up to 24 h ofincubation with pNP-caprylate pF2F4-rumen pUC-rumen (97 Mb screened) (95Mb screened) Culture supernatants, 1 0 IPTG-induced Cell lysis,IPTG-induced 6 1 Culture supernatants, 0 — arabinose-induced Cell lysis,arabinose- 5 — induced Total 12 1 Total minus hits occurring 10 1several timesHit Rate Comparison

In order to show that the 2-promoter system in pF2F4 is superior to asimple lac promoter, a hit rate comparison was carried out. For this, atest screening for lipase/esterase activity was carried out withpNP-caprylate as substrate in cluster screening with ˜300 clones/well.The libraries used comprise fragmented metagenomic DNA, which wasobtained from sheep rumen flora and was cloned both in pF2F4 and inpUCwhite, a pUC18 derivative. The average insert lengths were 3.5 kb(pUC-rumen) or 3.7 kb (pF2F4-rumen). In the comparative screening, 101Mb or 99 Mb of cloned DNA was therefore covered. In this test screeningit was found that by a combination of strong promoters and promoterconvergence, with the same insert-DNA and screening method, a hit rate(1/9.7 Mbp to 1/92 Mbp) higher by a factor of 9.5 can be achievedrelative to a one-sided lac promoter system (pUC vector). As only doublethe hit rate would be expected from the convergent arrangement of thepromoters, the rest of the increase in hit rate must be attributable tothe promoter strength.

The foregoing description and examples have been set forth merely toillustrate the invention and are not intended to be limiting. Sincemodifications of the disclosed embodiments incorporating the spirit andsubstance of the invention may occur to persons skilled in the art, theinvention should be construed broadly to include all variations withinthe scope of the appended claims and equivalents thereof.

The invention claimed is:
 1. A method of expressing a DNA sequence or amixture of DNA sequences comprising: (i) providing an expression system,comprising an expression vector and a separate regulatory vector, theexpression vector comprising: two mutually independently inducible,convergent promoters P₁ (promoter 1) and P₂ (promoter 2), whereinbetween P₁ and P₂, an insertion sequence, positioned downstream of P₁and downstream of P₂, configured so that the expression of a DNAsequence cloned into the insertion sequence is transcribed either via P₁or P₂; wherein the insertion sequence comprises a polylinker and/or anintegration sequence adapted to facilitate integration of the DNAsequence by recombination; and the regulatory vector comprising: asequence encoding a first regulator (R₁) of the first promoter and/or asecond regulator (R₂) of the second promoter, (ii) cloning the DNAsequence into the polylinker and/or the integration sequence of theexpression vector to obtain a recombinant expression vector; (iii)subsequently transfecting or transforming the host organism comprisingthe regulatory vector with the recombinant expression vector obtained in(ii); and (iv) inducing expression of the proteins encoded by the DNAsequence by adding a first inductor (I₁) inducing an activation of theR₁ and/or adding a second inductor (I₂) inducing the activation of theR₂, wherein the expression vector without a DNA molecule cloned into theinsertion sequence comprises not more than 3000 base pairs.
 2. Themethod according to claim 1, wherein the I₁ and the I₂ are added tospatially separate partial cultures of the host organism obtained in(iii).
 3. A method of screening a DNA library for a DNA moleculeexpressing a molecule having an activity of interest comprising: (a)providing an expression system comprising; an expression vector and aregulatory vector, the expression vector comprising: two mutuallyindependently inducible, convergent promoters P₁ (first promoter) and P₂(second promoter 2), wherein between P₁ and P₂, an insertion sequence ispositioned downstream of P₁ and downstream of P₂, configured so that theexpression of a DNA sequence cloned into the insertion sequence istranscribed either via P₁ or P₂, wherein the insertion sequencecomprises a polylinker and/or an integration sequence adapted tofacilitate integration of the DNA sequence by recombination; and theregulatory vector comprising: a sequence encoding a first regulator (R₁)of the P₁ and/or a second regulator (R₂) of the P₂; (b) cloning DNAmolecules of the DNA library into the insertion sequence of theexpression vector to produce a population of expression vectorscomprising cloned DNA molecules, (c) transforming or transfecting a hostcell population with the population of expression vectors of step (b)wherein the host cell population comprises the regulatory vector, (d)expressing the DNA molecule cloned into the insertion sequence byinducing expression of the R₁ by adding a first inductor (I₁) and/or theR₂ by adding a second inductor (I₂), and (e) screening the host cellsfor the activity of interest, wherein the expression vector without aDNA molecule cloned into the insertion sequence comprises not more than3000 base pairs.
 4. The method according to claim 3, wherein theactivity of interest is a catalytic activity of a protein produced bythe expression of the DNA molecule cloned into the insertion sequence.5. The method according to claim 3, wherein the regulatory vector codesfor a Laci regulator and/or for an AraC regulator.
 6. The methodaccording to claim 3, wherein the regulatory vector further comprises atleast one gene for transfer-RNA of a host organism.
 7. The methodaccording to claim 6, wherein said gene for the transfer-RNA is selectedfrom the group consisting of argU, argW, ileX, gluT, leuW, proL, metT,thrT, tyrU, thrU and argX of E. coli, which recognize the codons AGG,AGA, AUA, CUA, CCC, GGA or CGG.
 8. The method according to claim 3,wherein the regulatory vector contains the gene LysS for the T7lysozyme.
 9. The method according to claim 3, wherein the R₁ and the R₂are activated in step (d) in separate partial cultures of thetransformed or transfected host cell population.
 10. The methodaccording to claim 3, wherein the P₁ is a T7 promoter and/or the P₂ isan ara promoter.
 11. The method according to claim 3, wherein theexpression vector codes for a first terminator (T₁) of the P₁ in readingdirection of the P₁ downstream of the insertion sequence and/or for asecond terminator (T₂) of the P₂ in reading direction of the P₂downstream of the insertion sequence.
 12. The method according to claim11, wherein the T₁ is a T7 terminator and/or the T₂ is a terminator forthe host RNA polymerase; or vice versa.
 13. The method according toclaim 11, wherein an additional gene lies between the P₁ and its T₁ inthe reading direction of the P₁; or an additional gene lies between theP₂ and its T₂ in the reading direction of the P₂.
 14. The methodaccording to claim 1, wherein the regulatory vector or parts thereof areintegrated into a genome of the host organism.
 15. The method accordingto claim 1, wherein the regulatory vector codes for a Lad regulatorand/or for an AraC regulator.
 16. The method according to claim 1,wherein the regulatory vector further comprises at least one gene fortransfer-RNA of a host organism.
 17. The method according to claim 16,wherein said gene for transfer-RNA is selected from the group consistingof argU, argW, ileX, gluT, leuW, proI, metT, thrT, tyrU, thrU and argXof E. coli, which recognize the codons AGG, AGA, AUA, CUA, CCC, GGA orCGG.
 18. The method according to claim 1, wherein the regulatory vectorcomprises gene LysS for T7 lysozyme.
 19. The method according to claim1, wherein the P₁ is a T7 promoter and/or the P₂ is an ara promoter. 20.The method according to claim 1, wherein the expression vector furthercodes for a first terminator (T₁) of the P₁ in reading direction of theP₁ downstream of the insertion sequence and/or for a second terminator(T₂) of the P₂ in reading direction of the P₂ downstream of theinsertion sequence.
 21. The method according to claim 20, wherein thefirst terminator is a T7 terminator and/or the second terminator is aterminator for the host RNA polymerase or vice versa.
 22. The methodaccording to claim 20, wherein an additional gene lies between the firstpromoter and the first terminator in the reading direction of the firstpromoter; or an additional gene lies between the second promoter and thesecond terminator in the reading direction of the second promoter. 23.The method according to claim 21, wherein an additional gene liesbetween the first promoter and the first terminator in the readingdirection of the first promoter; or an additional gene lies between thesecond promoter and the second terminator in the reading direction ofthe second promoter.
 24. The method according to claim 1, wherein morethan one expression vector is provided each expressing a sequence of themixture of DNA sequences.
 25. The method according to claim 1, whereinthe host organism is prior to the cloning in (ii) transfected ortransformed with the regulatory vector.
 26. The method according toclaim 1, wherein I₁ is an inductor for P₁, but not for P₂ and/or I₂ isan inductor for P₂, but not P₁.
 27. The method according to claim 14,wherein I₁ is an inductor for P₁, but not for P₂ and/or I₂ is aninductor for P₂, but not P₁.
 28. The method according to claim 3,wherein the host organism is prior to the cloning in (b) transfected ortransformed with the regulatory vector.
 29. The method according toclaim 3, wherein the regulatory vector or parts thereof are integratedinto a genome of the host organism.